3F7Z

X-ray Co-Crystal Structure of Glycogen Synthase Kinase 3beta in Complex with an Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3F7Z/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2008-11-10 Released: 2009-03-10
Deposition Author(s): Mol, C.D., Dougan, D.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.253 (Depositor), 0.240 (DCC)
R-Value Work:
0.203 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Design, synthesis and structure-activity relationships of 1,3,4-oxadiazole derivatives as novel inhibitors of glycogen synthase kinase-3beta.

Saitoh, M., Kunitomo, J., Kimura, E., Hayase, Y., Kobayashi, H., Uchiyama, N., Kawamoto, T., Tanaka, T., Mol, C.D., Dougan, D.R., Textor, G.S., Snell, G.P., Itoh, F.

(2009) Bioorg Med Chem 17: 2017-2029

PubMed: 19200745 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2009.01.019
Primary Citation of Related Structures:
3F7Z, 3F88

PubMed Abstract:
Glycogen synthase kinase-3beta (GSK-3beta) is implicated in abnormal hyperphosphorylation of tau protein and its inhibitors are expected to be a promising therapeutic agents for the treatment of Alzheimer's disease. Here we report design, synthesis and structure-activity relationships of a novel series of oxadiazole derivatives as GSK-3beta inhibitors. Among these inhibitors, compound 20x showed highly selective and potent GSK-3beta inhibitory activity in vitro and its binding mode was determined by obtaining the X-ray co-crystal structure of 20x and GSK-3beta.

Organizational Affiliation

Pharmaceutical Research Division, Medicinal Chemistry Research Laboratories, Takeda Pharmaceutical Company, Ltd, Osaka, Japan. Saitoh_Morihisa@takeda.co.jp

Macromolecule Content

Total Structure Weight: 80.49 kDa
Atom Count: 5,716
Modelled Residue Count: 680
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	350	Homo sapiens	Mutation(s): 0 Gene Names: GSK3B EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841 Go to UniProtKB: P49841
PHAROS: P49841 GTEx: ENSG00000082701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
34O Query on 34O Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-(1,3-benzodioxol-5-yl)-5-[(3-fluoro-4-methoxybenzyl)sulfanyl]-1,3,4-oxadiazole C₁₇ H₁₃ F N₂ O₄ S TUTZKAQTSPMEBI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
34O	BindingDB: 3F7Z	IC50: 65 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253 (Depositor), 0.240 (DCC)
R-Value Work: 0.203 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.622	α = 90
b = 117.23	β = 102.71
c = 67.351	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Mol, C.D.

Dougan, D.R.

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-27
Changes: Structure summary